Contacts of the strand formed by residues 196 - 201 (chain E) in PDB entry 2SGD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 196 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43E SER 3.6 4.2 - - - +
45E GLY* 2.9 26.5 + - - -
54E THR* 3.8 5.0 - - - -
55E ALA* 3.4 29.6 - - - +
194E ASP 3.4 0.2 + - - -
195E SER* 1.3 67.9 - - - +
197E GLY* 1.4 62.3 + - - +
212E LEU* 3.9 7.6 - - - +
213E THR* 2.9 23.1 + - - -
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Residues in contact with GLY 197 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E SER* 3.9 6.7 - - - -
44E LEU 3.8 6.1 - - - -
45E GLY* 4.1 0.2 - - - -
139E ARG 3.4 11.2 - - - -
194E ASP 3.0 14.7 + - - -
195E SER 3.3 1.8 + - - -
196E GLY* 1.4 79.4 - - - +
198E PRO* 1.3 72.5 - - - +
212E LEU* 3.4 2.8 - - - -
213E THR* 2.8 30.4 + - - -
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Residues in contact with PRO 198 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E GLY 3.8 0.7 - - - -
19E GLY* 3.2 22.7 - - - +
44E LEU 3.5 4.3 - - - +
45E GLY* 3.4 19.0 - - - +
46E PHE* 3.5 22.4 - - + -
119E VAL* 3.5 33.9 - - + -
137E THR 3.8 0.9 - - - +
138E ARG* 3.3 7.3 - - - +
139E ARG* 3.2 35.6 + - + +
196E GLY 3.9 0.2 - - - -
197E GLY* 1.3 83.9 - - - +
199E LEU* 1.3 59.7 + - - +
200E TYR* 4.1 3.7 - - + -
211E GLY 3.8 5.2 - - - +
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Residues in contact with LEU 199 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E PHE* 3.5 3.6 - - - -
136E VAL* 3.2 43.1 - - + -
137E THR 3.4 17.0 - - - +
138E ARG* 4.2 3.4 - - + -
162E VAL* 5.3 0.2 - - + -
181E ILE* 4.8 6.5 - - + -
183E THR* 4.5 4.7 - - + -
190E VAL* 4.6 3.6 - - + -
197E GLY 3.8 0.2 + - - -
198E PRO* 1.3 70.7 - - - +
200E TYR* 1.3 54.0 + - - +
210E ILE* 2.7 51.2 + - + -
211E GLY 2.7 22.7 + - - +
228E PHE* 3.4 59.9 - - + -
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Residues in contact with TYR 200 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46E PHE* 4.7 2.7 - - + -
119E VAL* 3.6 34.7 + - + +
122E GLN* 3.6 26.2 - - + +
124E ILE* 3.9 18.8 - - + -
136E VAL* 3.2 7.1 - - - +
137E THR* 2.8 73.9 + - + +
138E ARG 4.5 1.1 - - - -
139E ARG* 4.6 5.6 - - + +
157E THR* 4.5 8.3 + - - +
198E PRO* 4.1 8.5 - - + -
199E LEU* 1.3 74.4 - - - +
201E SER* 1.3 59.0 + - - +
202E GLY 3.5 21.5 - - - -
208E ARG 3.1 17.0 - - - +
209E ALA* 4.3 2.2 - - - -
210E ILE* 3.8 5.8 - - - -
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Residues in contact with SER 201 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E MET* 4.0 5.7 - - - +
135E ALA 2.9 25.3 + - - -
136E VAL* 4.4 0.9 - - - +
137E THR* 5.1 2.2 - - - +
200E TYR* 1.3 78.0 - - - +
202E GLY* 1.3 64.6 + - - +
207E THR 3.1 0.5 + - - -
208E ARG* 2.9 57.4 + - - +
210E ILE* 4.1 12.3 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il